Zinc in PDB 5uwm: Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A, PDB code: 5uwm was solved by A.B.Taylor, X.Cao, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.77 / 1.62
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	140.073, 140.073, 46.860, 90.00, 90.00, 120.00
R / Rfree (%)	12.9 / 17.8

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A (pdb code 5uwm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A, PDB code: 5uwm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.8 occ:1.00 NE2 A:HIS226 2.0 9.4 1.0 OXT C:ASN215 2.0 19.3 1.0 NE2 A:HIS222 2.0 15.7 1.0 NE2 A:HIS232 2.1 17.2 1.0 C C:ASN215 2.6 17.6 1.0 O C:ASN215 2.7 16.8 1.0 CE1 A:HIS226 2.9 16.1 1.0 CE1 A:HIS222 3.0 16.1 1.0 CD2 A:HIS232 3.0 16.6 1.0 CD2 A:HIS226 3.0 16.6 1.0 CD2 A:HIS222 3.0 14.4 1.0 CE1 A:HIS232 3.0 15.9 1.0 CA C:ASN215 4.1 13.6 1.0 O A:HOH481 4.1 18.0 1.0 ND1 A:HIS226 4.1 16.3 1.0 ND1 A:HIS222 4.1 15.5 1.0 ND1 A:HIS232 4.1 16.2 1.0 CG A:HIS232 4.1 17.3 1.0 CG A:HIS226 4.1 17.2 1.0 CG A:HIS222 4.2 17.7 1.0 N C:ASN215 4.4 14.0 1.0 C13 A:8OA306 4.6 16.3 1.0 CE A:MET240 4.7 15.9 1.0 C C:LEU214 4.7 12.6 1.0 C14 A:8OA306 4.8 15.5 1.0 CB C:LEU214 4.8 20.2 1.0 OE2 A:GLU223 4.8 18.1 1.0 CB C:ASN215 4.9 15.9 1.0 O C:LEU214 4.9 17.1 1.0 C12 A:8OA306 4.9 16.6 1.0

Zinc binding site 2 out of 4 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:17.9 occ:1.00 NE2 A:HIS172 2.0 17.6 1.0 NE2 A:HIS187 2.0 16.7 1.0 OD2 A:ASP174 2.0 19.5 1.0 ND1 A:HIS200 2.0 16.6 1.0 CE1 A:HIS187 2.9 16.6 1.0 CG A:ASP174 2.9 18.8 1.0 CE1 A:HIS200 2.9 17.5 1.0 CD2 A:HIS172 3.0 15.4 1.0 CE1 A:HIS172 3.0 16.1 1.0 CG A:HIS200 3.1 17.2 1.0 CD2 A:HIS187 3.1 17.0 1.0 OD1 A:ASP174 3.2 22.6 1.0 CB A:HIS200 3.5 16.0 1.0 ND1 A:HIS187 4.1 18.5 1.0 O A:TYR176 4.1 19.0 1.0 NE2 A:HIS200 4.1 16.8 1.0 ND1 A:HIS172 4.1 16.6 1.0 CG A:HIS172 4.1 17.0 1.0 CD2 A:HIS200 4.2 17.1 1.0 CG A:HIS187 4.2 15.7 1.0 CB A:ASP174 4.3 18.1 1.0 CE1 A:PHE189 4.6 22.1 1.0 CZ A:PHE178 4.6 16.1 1.0 CE2 A:PHE178 4.8 18.1 1.0 O A:HOH439 4.9 16.1 1.0 CZ A:PHE189 4.9 22.6 1.0 CB A:TYR176 4.9 18.9 1.0 CA A:HIS200 5.0 13.6 1.0

Zinc binding site 3 out of 4 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:16.2 occ:1.00 O D:ASN215 2.0 15.8 1.0 NE2 B:HIS222 2.0 14.6 1.0 NE2 B:HIS232 2.1 14.8 1.0 NE2 B:HIS226 2.1 16.9 1.0 C D:ASN215 2.7 16.2 1.0 OXT D:ASN215 2.7 16.4 1.0 CD2 B:HIS222 3.0 16.1 1.0 CE1 B:HIS222 3.0 17.4 1.0 CE1 B:HIS232 3.0 15.3 1.0 CD2 B:HIS232 3.0 15.1 1.0 CE1 B:HIS226 3.1 18.1 1.0 CD2 B:HIS226 3.1 15.1 1.0 O B:HOH465 4.1 15.7 1.0 CA D:ASN215 4.1 15.3 1.0 ND1 B:HIS222 4.1 15.4 1.0 ND1 B:HIS232 4.1 15.8 1.0 CG B:HIS222 4.1 15.2 1.0 CG B:HIS232 4.2 14.5 1.0 ND1 B:HIS226 4.2 18.7 1.0 CG B:HIS226 4.3 16.2 1.0 N D:ASN215 4.4 14.2 1.0 CE B:MET240 4.6 19.5 1.0 C D:LEU214 4.8 16.3 0.5 C D:LEU214 4.8 16.4 0.5 C13 B:8OA306 4.8 14.7 1.0 C14 B:8OA306 4.9 14.9 1.0 CB D:ASN215 4.9 14.6 1.0 OE2 B:GLU223 4.9 18.4 1.0 CB D:LEU214 4.9 18.4 0.5 CB D:LEU214 4.9 18.7 0.5 O D:LEU214 5.0 16.1 0.5 O D:LEU214 5.0 16.7 0.5

Zinc binding site 4 out of 4 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (R)-17A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:17.3 occ:1.00 OD2 B:ASP174 2.0 18.4 1.0 NE2 B:HIS172 2.0 13.9 1.0 ND1 B:HIS200 2.1 16.3 1.0 NE2 B:HIS187 2.1 15.8 1.0 CD2 B:HIS172 2.9 17.3 1.0 CG B:ASP174 2.9 18.6 1.0 CE1 B:HIS200 3.0 16.4 1.0 CE1 B:HIS187 3.0 16.6 1.0 CE1 B:HIS172 3.1 17.1 1.0 CG B:HIS200 3.1 15.8 1.0 CD2 B:HIS187 3.1 14.3 1.0 OD1 B:ASP174 3.2 19.2 1.0 CB B:HIS200 3.5 15.1 1.0 CG B:HIS172 4.1 14.8 1.0 NE2 B:HIS200 4.1 15.9 1.0 ND1 B:HIS187 4.1 13.4 1.0 ND1 B:HIS172 4.1 18.2 1.0 CD2 B:HIS200 4.2 14.5 1.0 CG B:HIS187 4.2 13.6 1.0 O B:TYR176 4.3 16.7 1.0 CB B:ASP174 4.3 18.9 1.0 CE1 B:PHE189 4.5 21.2 1.0 CZ B:PHE178 4.6 16.0 1.0 CZ B:PHE189 4.8 23.1 1.0 CE2 B:PHE178 4.8 15.7 1.0 O B:HOH468 4.9 17.4 1.0 CA B:HIS200 5.0 12.8 1.0

J.Y.Choi, R.Fuerst, A.M.Knapinska, A.B.Taylor, L.Smith, X.Cao, P.J.Hart, G.B.Fields, W.R.Roush. Structure-Based Design and Synthesis of Potent and Selective Matrix Metalloproteinase 13 Inhibitors. J. Med. Chem. V. 60 5816 2017.
ISSN: ISSN 1520-4804
PubMed: 28653849
DOI: 10.1021/ACS.JMEDCHEM.7B00514